name about category URL
3dslicer multi-platform, free and open source software package for visualization and medical image computing Graphics
454 sequencing data analysis software Bioinformatics
R free software environment for statistical computing and graphics Data Analysis
a2ps any to postscript System Tools
abaqus finite element analysis Physics
abyss de nono sequence assembler intended for short paired-end reads and large genomes Bioinformatics
adapterremoval rapid adapter trimming, identification, and read merging Bioinformatics
ale Assembly Likelihood Estimator Bioinformatics
aligngraph Algorithm for secondary de novo genome assembly guided by closely related references Bioinformatics
allpathslg high quality genome assembly from low cost data Bioinformatics
amber assisted model building with energy refinement Molecular Biology
amira a powerful, multifaceted 3D software platform for visualizing, manipulating, and understanding biomedical data coming from all types of sources and modalities Graphics
anaconda scientific python distribution Programming Tools
anaconda3 scientific python distribution Programming Tools
analysis evolutionary genetic analysis Bioinformatics
ant Java Library and Command Line Tool for building packages Programming Tools
ants Advanced Normalization Tools (ANTs) extracts information from complex datasets that include imaging Libraries
arden2bytecode language to represent medical knowledge Bioinformatics
arem peak caller for ChIP-Seq experiments that robustly handles short readds with multiple possible mappings Bioinformatics
argparse argparse Libraries
armadillo C++ linear algebra library Libraries
arpack collection of Fortran77 subroutines designed to solve large scale eigenvalue problems Libraries
arrayfire ArrayFire is a high-performance software library designed for maximum productivity and speed without the hassle of writing difficult low-level device code. Libraries
ase Atomistic Simulation Environment Molecular Biology
aspera high performance file transfer Accessories
astrobear Collection of libraries used by astrobear Libraries
astropy community python library for astronomy Physics
atk accessibility toolkit Libraries
atlas automatically tuned linear algebra software Mathematics
audacity audio editor Accessories
autoconf generate configure scripts Programming Tools
autodockvina molecular docking and virtual screening Molecular Biology
automake generate files Programming Tools
avogadro molecule editor and visualizer Chemistry
bali-phy bayesian alignment and phylogeny estimation Bioinformatics
bam2x extract info from bam files Bioinformatics
bamtools API and command line toolkit for working with BAM data Bioinformatics
basespace-cli BaseSpace Sequence Hub Bioinformatics
bazel build tool Programming Tools
bbcp file transfer client Internet
bbmap BBMap short read aligned and other bioinformatic tools Bioinformatics
bcftools program for variant calling and manipulating VCFs and BCFs Bioinformatics
bcl2fastq bcl conversion and multiplexing Bioinformatics
beacon automated tool for Bacterial gEnome Annotation ComparisON Bioinformatics
bear2fix Routines for analyzing hdf5 files produced by astrobear Physics
beast2 Bayesian Evolutionary Analysis by Sampling Trees Bioinformatics
bedops fast, highly scalable and easily-parallelizable genome analysis toolkit Bioinformatics
bedtools genome arithmetic suite Bioinformatics
bfast Blat-like Fast Accurate Search Tool Bioinformatics
bioformats Tools for manipulating open microscopy formats Libraries
biom-format a general-use format for representing biological sample by observation contingency tables Bioinformatics
bioperl Perl code useful in biology Bioinformatics
biopython tools for biological computation Libraries
bioxtasraw analysis of small angle x-ray scattering data Chemistry
bismark bisulfite read mapper and methylation caller Bioinformatics
bison General-purpose parser generator Libraries
blas Basic Linear Algebra Subprograms Libraries
blasr PacBio long read aligner Bioinformatics
blast basic local alignment search tool Bioinformatics
blat BLAST-like alignment tool Bioinformatics
bonnie benchmark suite System Tools
boost portable C++ source libraries Libraries
bowtie ultrafast memory-efficient short read aligner Bioinformatics
bowtie2 ultrafast memory-efficient short read aligner Bioinformatics
breakdancer genome-wide detection of structural variants from next generation paired-end sequencing reads Bioinformatics
brownie reference based error correction Bioinformatics
bwa Burrows-Wheeler aligner Bioinformatics
bwidget TCL widget library Programming Tools
bwtool command-line utility for bigWig files Bioinformatics
bzip2 compression System Tools
caffe deep learning framework Computer Science
cairo 2D graphics library with support for multiple output devices Libraries
canu fork of Celera Assembler, designed for high-noise single-molecule sequencing Bioinformatics
catdoc read MS Word and Excel files Accessories
cdec decoder, aligner, and learning framework for statistical machine translation and similar prediction models Computer Science
cdo Climate Data Operators Physics
ceas cis-regulatory element annotation system Bioinformatics
cgal Computational Geometry Algorithms Library Libraries
chimera visualization of molecular structures Chemistry
circos circular genome variation and data visualization tool Graphics
cisa contig integrator for sequence assembly Bioinformatics
cistrome platform for transcriptional regulation studies Bioinformatics
clapack f2c'd version of LAPACK Libraries
clustalw multiple sequence alignment Bioinformatics
clustalx multiple sequence alignment Bioinformatics
cmake an extensible, open-source system that manages the build process in an operating system System Tools
commet COmpare Multiple METagenomes Bioinformatics
comsol multiphysics simulation Physics
conifer copy number inference from exome reads Bioinformatics
convert ImageMagick Convert utility System Tools
corenlp Java viewer for chemical structures in 3D Chemistry
corset clustering de novo assembled transcripts and counting overlapping reads Bioinformatics
cp2k program to perform atomistic and molecular simulations of solid state, liquid, molecular, and biological systems Chemistry
cpc Coding Potential Calculator Bioinformatics
cpmd Car-Parrinello Molecular Dynamics Chemistry
crisp code for multi-sample variant calling from sequence data Bioinformatics
crispresso analysis of CRISPR-Cas9 genome editing outcomes from sequencing data Bioinformatics
ctm C implementation of the correlated topic model (CTM) Mathematics
cuda CUDA Software Development Kit (gcc 4.4.7) Programming Tools
cudamat Python module for performing basic dense linear algebra computations on the CPU using CUDA Libraries
cudnn GPU-accelerated library for deep neural networks Programming Tools
cufflinks transcript assembly, differential expression, and differential regulation for RNA-Seq Bioinformatics
curl multiprotocol file transfer library Internet
cushaw gapped short-read alignment Bioinformatics
cutadapt removes adapter sequences from DNA sequencing reads Bioinformatics
cytoscape network visualization Graphics
db Berkeley DB Libraries
dbg2olc assembly of large genomes using long erroneous reads of the third generation sequencing technologies Bioinformatics
dcs client application designed to be run locally on a data producer's machine System Tools
ddimap DDiMap Bioinformatics
dealii open source finite element library Libraries
deeptools tools for exploring deep sequencing data Bioinformatics
dendropy phylogenetic computing Bioinformatics
device advanced, finite element multiphysics simulation environment Physics
dftb fast approximate DFT for molecules Chemistry
diffsplice genome-wide detection of differential splicing events with RNA-seq Bioinformatics
digits Deep Learning GPU Training System Computer Science
disperse Automatic identification of persistent structures Mathematics
dock molecular docking Chemistry
dofe distribution of fitness effects and rates of adaptive substitution Bioinformatics
dptools Processing and converting data related to the DFTB+ package Chemistry
drmaa-slurm DRMAA for Slurm Libraries
duc File usage analyzer System Tools
ea-utils Command-line tools for processing biological sequencing data Libraries
eclipse integrated development environment Programming Tools
eigen C++ template library for linear algebra Libraries
elan annotations on video and audio resources Computer Science
elfutils collection of utilities and libraries to read, create and modify ELF binary files, find and handle DWARF debug data, symbols, thread state and stacktraces for processes and core files on GNU/Linux Programming Tools
emacs extensible, customizable text editor Accessories
emboss European Molecular Biology Open Software Suite Bioinformatics
ensembl-tools variant effect predictor Bioinformatics
epstool Epstool is a utility to create or extract preview images in EPS files, fix bounding boxes and convert to bitmaps Accessories
exabayes bayesian tree inference Bioinformatics
examl Exascale Maximum Likelihood (ExaML) code for phylogenetic inference using MPI Bioinformatics
exonerate a generic tool for pairwise sequence comparison Libraries
expat Expat XML parser Libraries
expect automate interactive applications System Tools
express streaming tool for quantifying the abundances of a set of target sequences from sampled subsequences Bioinformatics
falcon experimental PacBio diploid assembler Bioinformatics
fastqc quality control tool for high throughput sequence data Bioinformatics
fastx FASTQ/A short-reads pre-processing tools Bioinformatics
fdtd-solutions Single and multi-processor finite-difference time-domain optical design Physics
fenics solution of differential equations Mathematics
ferret visualization and analysis environment for studying climate Graphics
ffi portable, high level programming interface to various calling conventions Libraries
ffmpeg A complete, cross-platform solution to record, convert and stream audio and video Graphics
fftw2 FFTW library for computing the discrete Fourier transform (DFT) Libraries
fftw3 FFTW3 library for computing the discrete Fourier transform (DFT) Libraries
figtree molecular evolution, phylogenetics, and epidemiology Bioinformatics
fiji Fiji is just ImageJ with plugins Graphics
findutils basic directory searchiing utilities System Tools
firefox web browser Internet
flash merge mates from fragments that are shorter than twice the read length Bioinformatics
flens flexible library for efficient numerical solutions Mathematics
flex the fast lexical analyser Libraries
flowgate free software environment for statistical computing and graphics Data Analysis
fltk a cross-platform C++ GUI toolkit Libraries
freebayes Bayesian haplotype-based polymorphism discovery and genotyping Bioinformatics
freeglut OpenSourced alternative to the OpenGL Utility Toolkit (GLUT) library Libraries
freesurfer processing and analyzing brain MRI images Graphics
freetype freely available software library to render fonts Libraries
freexl library to extract valid data from within an Excel spreadsheet Libraries
fsl analysis tools for FMRI, MRI, and DTI brain imaging data Bioinformatics
gam-ngs genomic assemblies merger for NGS Bioinformatics
gamess general atomic and molecular electronic structure system Chemistry
gap2seq filling gaps in scaffolds produced by genome assembly tools Bioinformatics
gapfiller close gaps produced by a scaffolding program using one or more mate pairs or paired-end libraries Bioinformatics
gatb Genome Assembly Tool Box Bioinformatics
gatk genome analysis toolkit Bioinformatics
gaussian quantum chemistry Chemistry
gcc GNU compiler collection Programming Tools
gcta genome-wide complex trait analysis Bioinformatics
gdal translator library for raster and vector geospatial data formats Physics
gdc-client GDC data transfer tool Accessories
gdk-pixbuf toolkit for image loading and pixel buffer manipulation Libraries
gem5 modular platform for computer system architecture research Programming Tools
geneious bioinformatics tools Bioinformatics
genepattern computational biology open-source package Bioinformatics
genetorrent downloading sequence data Bioinformatics
genometools open source genome analysis software Bioinformatics
geos geometry engine, open source Graphics
gephi open graph viz platform Graphics
gffcompare classify, merge, tracking, and annotation of GFF files by comparing to a reference annotation GFF Bioinformatics
gflags command line flags processing Programming Tools
ghc Glasgow Haskell Compiler Programming Tools
ghostscript Interpreter for the PostScript language and for PDF Graphics
git distributed version control system Programming Tools
git-lfs Git large file storage Programming Tools
gl2ps an OpenGL to PostScript printing library Libraries
glew OpenGL Extension Wrangler Library Libraries
glfw free, Open Source, multi-platform library for creating windows with OpenGL or OpenGL ES contexts and receiving many kinds of input Libraries
glib a low-level libraries useful for providing data structure handling for C Libraries
glibc GNU C library Libraries
glog google logging module Programming Tools
glpk GNU Linear Programming Kit Libraries
gmap a genomic mapping and alignment program for mRNA and EST sequences Bioinformatics
gmp GNU Multiple Precision Arithmetic Library Libraries
gmt Generic Mapping Tools: open source collection of about 80 command-line tools for manipulating geographic and Cartesian data sets Physics
gnat GNU Ada compiler Programming Tools
gnumpy Python interface to GPUs and numpy Libraries
gnuplot plotting program Graphics
gnutls secure communications library implementing the SSL, TLS and DTLS protocols and technologies around them Libraries
gobject-instrospection middleware layer between C libraries (using GObject) and language bindings Libraries
gpaw density-functional theory (DFT) Python code based on the projector-augmented wave (PAW) method and the atomic simulation environment (ASE) Molecular Biology
gperf perfect hash function generator System Tools
gpfw free, Open Source, multi-platform library for creating windows with OpenGL or OpenGL ES contexts and receiving many kinds of input Libraries
grace WYSIWYG 2D plotting tool Graphics
graphiz open source graph visualization software Graphics
graphlan circular representations of taxonomic and phylogenetic trees Bioinformatics
gromacs molecular dynamics Molecular Biology
gromacswrapper python package that wraps system calls to Gromacs tools into thin classes Chemistry
gshrimp image processing Data Analysis
gsl GNU scientific library Libraries
gstreamer library for constructing graphs of media-handling components Libraries
gstreamer-plugins gstreamer Libraries
gtk Gimp Toolkit:A multi-platform toolkit for creating graphical user interfaces Libraries
guile GNU Ubiquitous Intelligent Language for Extensions Programming Tools
gurobi optimizer Mathematics
h5py HDF5 for Python Libraries
h5utils set of utilities for visualization and conversion of scientific data in the free, portable HDF5 format Libraries
hal hierarchical alignment format Bioinformatics
harfbuzz an OpenType text shaping engine Libraries
harminv a free program (and accompanying library) to solve the problem of harmonic inversion Mathematics
hdf4 a library and multi-object file format for storing and managing data between machines Libraries
hdf5 data model, library, file format Libraries
hdfview HDF file viewer System Tools
hg Mercurial Revision Control System System Tools
hisat graph-based alignment of next generation sequencing reads to a population of genomes Bioinformatics
hmmer biosequence analysis using profile hidden Markov models Bioinformatics
homer motif discovery and next-gen sequencing analysis Bioinformatics
hoomd General purpose particle simulation toolkit Libraries
hpctoolkit High performance computing toolkit Programming Tools
hpctraceviewer GUI for hpctoolkit Programming Tools
hpcviewer GUI for hpctoolkit Programming Tools
htseq analysis of high-throughput sequencing data Bioinformatics http://www-huber/
htslib library for reading/writing high-throughput sequencing data Bioinformatics
hyphy hypothesis testing using phylogenies Bioinformatics
hypre a library for solving large, sparse linear systems of equations on massively parallel computers Libraries
idl scientific programming language Data Analysis
idp isoform detection and prediction Bioinformatics
igv integrative genomics viewer Bioinformatics
ilmbase Industrial Light & Magic base libraries Libraries
imagemagick image processing Libraries
impi Intel MPI Programming Tools
impute genotype imputation and haplotype phasing Bioinformatics
imsl mathematical and statistical functions Libraries
infernal Infernal (INFERence of RNA ALignment) is for searching DNA sequence databases for RNA structure and sequence similarities Bioinformatics
inkscape A powerful, free design tool Graphics
intel Intel utilities Programming Tools
intelpython intel python Programming Tools
intelpython3 intel python Programming Tools
iozone filesystem benchmarking System Tools
ipm integrated performance modeling Programming Tools
ipyrad Interactive assembly and analysis of RAD-seq data sets Bioinformatics
ipython Interactive Python Programming Tools
iqtree phylogenomics by maximum likelihood Bioinformatics
itk open-source, cross-platform system that provides developers with an extensive suite of software tools for image analysis Libraries
j3d java 3D library Libraries
jabba read error correction tool for PacBio data Bioinformatics
jags Just Another Gibbs Sampler Data Analysis
jamg just annotate my genome Bioinformatics
japsa Just Another JAva Package for Sequence Analysis Bioinformatics
jasper Open source JPEG-2000 part 1 codec Graphics
java Java pre-release development kit Programming Tools
jdk Java development kit Programming Tools
jellyfish fast parallel k-mer counting for DNA Bioinformatics
jmol Java viewer for chemical structures in 3D Chemistry
jpeg free library for JPEG image compression Libraries
jre Java pre-release development kit Programming Tools
jruby ruby programming language on the Java virtual machine Programming Tools
julia high-level, high-performance dynamic programming language Programming Tools
jupyter Interactive Python Programming Tools
jupyterhub multiuser version of the notebook designed for centralized deployments in companies, university classrooms and research labs Programming Tools
kallisto program for quantifying abundances of transcripts from RNA-Seq data Bioinformatics
karect KAUST assembly read error correction tool Bioinformatics
kenlm estimates, filters, and queries language models Libraries
kentutils UCSC command line bioinformatics utilities Bioinformatics
khmer nucleotide sequence k-mer counting, filtering, graph traversal Bioinformatics
lammps molecular dynamics Chemistry
lapack linear algebra package Libraries
last genome-scale sequence comparison Bioinformatics
latex2html bringing high quality documents to the web Accessories
lcms littlc cms color engine Libraries
leveldb lightweight single purpose library for persistence with bindings Data Analysis
lftp sophisticated ftp/http client, and a file transfer program supporting a number of network protocols System Tools
libav a friendly and community-driven effort to provide its users with a set of portable, functional and high-performance libraries for dealing with multimedia formats of all sorts Libraries
libcanberra implementation of the XDG Sound Theme and Name Specifications, for generating event sounds on free desktops, such as GNOME Libraries
libctl Guile-based library implementing flexible control files for scientific simulations Libraries
libevent The libevent API provides a mechanism to execute a callback function when a specific event occurs on a file descriptor or after a timeout has been reached Libraries
libffi Foreign Function Interface Libraries
libgd open source code library for the dynamic creation of images by programmers Libraries
libglew The OpenGL Extension Wrangler Library Libraries
libgpuarray library to manipulate tensors on the GPU Libraries
libjpeg-turbo JPEG image codec that uses SIMD instructions to accelerate baseline JPEG compression and decompression Libraries
libmatheval parse and evaluate symbolic expressions input as text Libraries
libogg a multimedia container format, and the native file and stream format for the multimedia codecs Libraries
libpng the free reference library for reading and writing PNGs Libraries
libreoffice free office suite Accessories
libsequence C++ class library for evolutionary genetic analysis Bioinformatics
libsndfile library for reading files containing sampled sound Libraries
libtasn1 ASN.1 library used by GnuTLS, GNU Shishi Libraries
libtool The GNU Portable Library Tool Libraries
libunwind unwinding library Programming Tools
libvorbis reference implementation of the Vorbis codec Libraries
libxc exchange-correlation functionals for density functional theory Chemistry
libzip C library for reading, creating, and modifying zip archives Libraries
liggghts discrete element method particle simulation code Physics
links long interval nucleotide K-mer scaffolder Bioinformatics
lmdb lightning memory-mapped database manager Data Analysis
locarna global and local alignment of RNA Bioinformatics
loos lightweight object-oriented structure library Molecular Biology
lordec hybrid error correction program for long PacBio reads Bioinformatics
lpp pre- and post-processing capability for the LAMMPS molecular dynamics package Physics
lsc long range error correction tool Bioinformatics
luajit just-in-time compiler for lua Programming Tools
lumpy a general probabilistic framework for structural variant discovery Bioinformatics
lxtask Lightweight X Task manager System Tools
m4 Unix Macro Processor Libraries
macs model-based analysis for ChIP-Seq Bioinformatics
magma GPU accelerated linear algebra Libraries
magmaca MAGMA computer algebra system Mathematics
maker genome annotation pipeline Bioinformatics
marginalign UCSC Nanopore Bioinformatics
masurca whole genome assembly Bioinformatics
mathematica computation, symbolic mathematics, and visualization Mathematics
matlab MATLAB (matrix laboratory) is a multi-paradigm numerical computing environment and fourth-generation programming language Mathematics
matlab-runtime matlab runtime environment Mathematics
matplotlib python 2D plotting library Libraries
mc Midnight Commander System Tools
md5deep compute checksums on arbitrary number of files Accessories
mdbtools work with files from Microsoft Access Libraries
meep a free finite-difference time-domain (FDTD) simulation software package developed at MIT to model electromagnetic systems Physics
mega molecular evolutionary genetics analysis Bioinformatics
megahit ultra-fast single-node solution for large and complex metagenomics assembly Bioinformatics
meld visual diff and merge tool Programming Tools
meme fast parallel k-mer counting for DNA Bioinformatics
mesa 3D graphics library Libraries
metabat tool for accurately reconstructing single genomes from complex microbial communities Bioinformatics
mfold RNA secondary structure prediction Molecular Biology
mgiza A word alignment tool based on famous GIZA++, extended to support multi-threading, resume training and incremental training Computer Science
mgltools Molecular Graphics Library Tools Molecular Biology
mgtaxa taxonomic classification of metagenomic sequences with machine learning Bioinformatics
miniasm ultrafast de novo assembly for long noisy reads (though having no consensus step) Bioinformatics
minimap experimental tool to find approximate mapping positions between long sequences Bioinformatics
misopy mixture of isoforms module for isoform quantification using RNA-Seq Bioinformatics http://pypi.pyhon/org/pypi/misopy
mitoprot prediction of mitochondrial targeting sequences Bioinformatics
mkl-boost MKL boost Libraries
molcas ab initio quantum chemistry software package Chemistry
molden pre and post processing program for molecular and electronic structure Chemistry
molstat a collection of tools for simulating and understanding single molecule behavior Chemistry
mongodb cross-platform document-oriented NoSQL database Data Analysis
moose multiphysics object-oriented simulation environment Physics
mopac semiempirical quantum chemistry Chemistry
mosh remote terminal application allowing roaming, intermittent connectivity, local echo Internet
mpb MIT photonic bands Physics
mpc C library for the arithmetic of complex numbers with arbitrarily high precision and correct rounding of the result Libraries
mpfr multiple precision floating point library Libraries
mpiblast freely available, open- Libraries
mpich high performance and widely portably implementation of the Message Passing Interface standard Programming Tools
mpip lightweight, scalable MPI profiling Programming Tools
mplus latent variable modeling program Data Analysis
mrbayes bayesian inference of phylogeny Bioinformatics
multiqc aggregate results from bioinformatics analyses across many samples into a single report Bioinformatics
mummer modular system for rapid whole genome alignment of finished or draft sequence Bioinformatics
muscle multiple sequence alignment Bioinformatics
mysql open source relational database management system Data Analysis
mysql-python interface for connecting to a MySQL database server from Python Libraries
mysql-workbench integrated tools environment for MySQL Data Analysis
namd scalable molecular dynamics Molecular Biology
nanocorr error correction for Oxford Nanopore data Bioinformatics
nanopolish Signal-level algorithms for MinION data Bioinformatics
nas hybrid approach to take advantage of data generated using MinION device Bioinformatics
ncftp FTP client System Tools
ncl NCAR command language Physics
nco NetCDF command operators Programming Tools
netcdf software libraries and self-describing, machine-independent data formats that support the creation, access, and sharing of array-oriented scientific data Libraries
netcdf-fortran software libraries and self-describing, machine-independent data formats that support the creation, access, and sharing of array-oriented scientific data Libraries
netlogo multi-agent programmable modeling environment Programming Tools
nettle cryptographic library that is designed to fit easily in more or less any context Libraries
nlopt nonlinear optimization Libraries
nodejs Event-driven I/O server-side JavaScript environment based on V8 System Tools
novocraft aligner for single-end and paired-end reads Bioinformatics
numpy fundamental package for scientific computing with Python Libraries
nupic hierarchical temporary memory Data Analysis
nwchem quantum chemistry Chemistry
ocaml OCAML programming language Programming Tools
ocproxy OpenConnect proxy Internet
octave high-level interpreted language, primarily intended for numerical computations Mathematics
octopus density functional theory Chemistry
omero OMERO is client-server software for visualization, management and analysis of biological microscope images. Microscopy
opacplot python package for manipulating Equation of State and Opacity data Chemistry
openbabel chemical toolbox Chemistry
openblas optimized BLAS library Libraries
opencl opencl headers Libraries
openconnect VPN client Internet
opencv Open Source Computer Vision Library Libraries
openexr High dynamic-range image file format Graphics
openmm toolkit for molecular simulation Molecular Biology
openmpi high performance message passing library Programming Tools
openms LC/MS data management and analyses Chemistry
opera optimal genome scaffolding program Bioinformatics
orca quantum chemistry Chemistry
orthodb database of orthologs Bioinformatics
orthomcl ortholog groups of protein sequences Bioinformatics
ortools Google's software suite for combinatorial optimization Libraries
ovito scientific visualization and analysis software for atomistic simulation data Graphics
p3dfft parallel three-dimensional fast Fourier transforms Libraries
p4est Parallel AMR on forests of octrees Libraries
p7zip file archiver System Tools
packmol packing optimization for molecular dynamics simulations Chemistry
paml phylogenetic analysis by maximum likelihood Bioinformatics
pamlx phylogenetic analysis by maximum likelihood Bioinformatics
pandoc universal document converter Accessories
pango library for laying out and rendering of text, with an emphasis on internationalization Libraries
parallel shell tool for executing jobs in parallel System Tools
paraview an open-source, multi-platform data analysis and visualization application Graphics
pbcore Python APIs for interacting with PacBio data files Bioinformatics
pbh5tools swiss-army knife for interrogating PacBio HDF5 files Bioinformatics
pbsuite automated pipeline to align long sequencing reads to high-confidence draft assembles Bioinformatics
pccalc calculates principal components for datasets with large sample sizes Bioinformatics
pcre Perl Compatible Regular Expressions Libraries
pdbdagcon sequence consensus Bioinformatics
peaksplitter subdivision of ChIP-seq/ChIP-chip regions into discrete signal peaks Bioinformatics
pear Illumina paired-end read and merger Bioinformatics
pecnv C++ tools for calling structural variants from PE mapping of short reads Bioinformatics
perf profiling with performance counters Programming Tools
perl Perl programming language Programming Tools
perl-modules perl modules Libraries
petsc portable, extensible toolkit for scientific computation Mathematics
petsc4py PETSc for python Mathematics
pgplot plotting library for fortran (gfortran 5.2.0) Libraries
pgx parallel graph analytics Computer Science
phantomjs Headless WebKit scriptable with a JavaScript API Internet
photoscan Commercial Photogrammetry software - bring your own license Data Analysis
php general-purpose scripting language Internet
phylocsf determine whether multi-species nucleotide alignment is likely to represent protein-coding region Bioinformatics
picard Java-based command-line utilities to manipulate SAM files Bioinformatics
picrust a bioinformatics software package designed to predict metagenome functional content from marker gene (e.g., 16S rRNA) surveys and full genomes Bioinformatics
pigz parallel implementation of gzip System Tools
pin binary instrumentation tool Programming Tools
pindel detection of breakpoints of deletions, insertions, inversions, duplications, and other structural variants Bioinformatics
pipipes piRNA pipeline collection developed in Zamore Lab Bioinformatics
pixman a low-level software library for pixel manipulation Libraries
plink whole genome association analysis toolset Bioinformatics
plumed open source library for free energy calculations Chemistry
pmw toolkit for building high-level compound widgets in Python using the Tkinter module Libraries
popbam population-based analyses of next-generation sequencing data Bioinformatics
popoolation compare allele frequencies for SNPs between two or more populations Bioinformatics
poreseq error correction and variant calling algorithm for nanopore sequencing Bioinformatics
poretools toolkit for working with nanopore sequencing data from Oxford Nanopore Bioinformatics
praat phonetics by computer Computer Science
probabel tools for genome-wide association analysis of imputed genetic data Bioinformatics
progressivecactus multiple genome aligner Bioinformatics
proovread PacBio hybrid error correction through iteractive short read consensus Bioinformatics
protobuf language neutral, platform neutral extensible mechanism for serializing structured data Programming Tools
provide program for viral diversity estimation Bioinformatics
psfj automatically analyses the full field-of-view (FOV) performance of a given fluorescence microscope/objective lens combination with respect to its optical resolution and chromatic aberrations Graphics
psi4conda open-source quantum chemistry Chemistry
pt3 analysis of time-resolved photon counting from PicoHarp 300 T3 mode files Chemistry
pybedtools wrapper for BEDTools Bioinformatics
pycifrw CIF/STAR file support for Python Chemistry
pycogent software library for genomic biology Bioinformatics
pycuda CUDA wrapper for python Programming Tools
pyfasta fast, memory-efficient, pythonic access to fasta sequence files Bioinformatics
pymol molecular visualization system on an open-source foundation Graphics
pyqtgraph python graphics and GUI utility Graphics
pysam python interface for SAM/BAM sequence alignment and mapping format Bioinformatics
pysamstats Python utility for calculating statistics against genome positions based on sequence alignments from a SAM or BAM file Bioinformatics
pyslurm Python interface to slurm 15.08.8 Libraries
pytables python package for managing hierarchical datasets Libraries
python Python programming language Programming Tools
python3 Python3 programming language Programming Tools
pyvcf variant call format reader Bioinformatics
pyxaid PYthon eXtension for Ab Initio Dynamics Chemistry
qctool quality control and analysis of gwas datasets Bioinformatics
qdmr quantitative differentially methylated region Bioinformatics
qe electronic-structure calculations Chemistry
qgis geographic information system Libraries
qhull computes the convex hull, Delaunay triangulation, Voronoi diagram, halfspace intersection about a point, furthest-site Delaunay triangulation, and furthest-site Voronoi diagram Mathematics
qiime Quantitative Insights into Microbial Ecology Molecular Biology
qiimetomaaslin convert Qiime output to MaAsLin input Bioinformatics
qrupdate Fortran library for fast updates of QR and Cholesky decompositions. Libraries
qt cross-platform application and UI framework for developers using C++ or QML Libraries
qtwebkit Qt port of WebKit Libraries
quast QUality ASessment Tool for Genome Assemblies Bioinformatics
r free software environment for statistical computing and graphics Data Analysis
raxml randomized axelerated maximum likelihood Bioinformatics
readline readline utility Libraries
realpath list contents of directories in a tree-like format System Tools
recon de novo algorithm for identification of repeat families from biological sequences Bioinformatics
repdenovo construct repeats directly from raw reads Bioinformatics
repeatmasker program that screens DNA sequences for interspersed repeats and low complexity DNA sequences Bioinformatics
repeatmodeler RepeatModeler is a de-novo repeat family identification and modeling package Bioinformatics
resqc RNA-seq quality control package Bioinformatics
retroseq discovery and genotyping of transposable element variants Bioinformatics
rh6 RHEL6 packages System Tools
rmagick Ruby+ImageMagick Libraries
rmats multivariate analysis of transcript splicing Bioinformatics
rmblast RepeatMasker compatible version of the standard NCBI BLAST suite Bioinformatics
rna-star spliced transcripts alignment to a reference Bioinformatics
rnastructure RNA and DNA secondary structure prediction and analysis Bioinformatics
rodeo A native Python IDE for Data Science Data Analysis
root A modular scientific software framework. It provides all the functionalities needed to deal with big data processing, statistical analysis, visualisation and storage. It is mainly written in C++ but integrated with other languages such as Python and R Data Analysis
rsem RNA-Seq by expectation maximization Bioinformatics
rstudio GUI for R Data Analysis
ruby dynamic, open source programming language with a focus on simplicity and productivity Programming Tools
sage open-source mathematics software system Mathematics
salmon highly accurate and wicked fast transcript-level quantification from RNA-seq reads using lightweight alignments Bioinformatics
sambamba Tools for working with SAM/BAM data Bioinformatics
samblaster samblaster: a tool to mark duplicates and extract discordant and split reads from sam files Bioinformatics
samstat displays various properties of next-generation sequencing reads stored in SAM/BAM format Bioinformatics
samtools utilities for sequence alignments Bioinformatics
sas data management Data Analysis
sbt an open source build tool for Scala and Java projects, similar to Javas Maven or Ant. Programming Tools
scala an object-functional programming and scripting language for general software applications Programming Tools
scarpa stand-alone scaffolding tool for NGS data Bioinformatics
schrodinger computational chemistry package Chemistry
scilab numerical computation Mathematics
scipy open source library of scientific tools Libraries
scons software construction tool Programming Tools
screen window manager Accessories
selectiontools Pipeline to take VCF through to Selection Analysis Bioinformatics
sendemail sending SMTP mail from command line System Tools
seqclean sequence cleaner Bioinformatics
seqtk toolkit for processing sequences in FASTA/Q formats Bioinformatics
sga string graph assembler Bioinformatics
shapeit estimation of haplotypes Bioinformatics
shm a powerful seismic waveform analysis tool Physics
shrimp SHort Read Mapping Package Bioinformatics
siesta electronic structure calculations Chemistry
singularity containers System Tools
slicer visualization and medical image computing Graphics
slurm Slurm job scheduler System Tools
smartgit SmartGit is a Git client with Mercurial and Subversion support. SmartGit is free for non-commercial use and runs on Mac OS X, Windows and Linux. Programming Tools
smufin somatic mutation finder Bioinformatics http://cg.bsc.ed/smufin
snappy fast compressor/decompressor System Tools
snptest analysis of single SNP association Bioinformatics
soapdenovo a short read de novo assembly tool, is a package for assembling short oligonucleotide into contigs and scaffolds Libraries
sopra assembler for mate pair/paired-end reads from high throughput sequencing platforms, e.g. Illumina and SOLiD Bioinformatics
sourcetracker Bayesian approach to estimating proportion of a novel community from a set of source environments Bioinformatics
soxr resampler library Libraries
spades genome assembler Bioinformatics
sparc sparsity-based consensus algorithm for long erroneous sequencing reads Bioinformatics
spark a fast and general-purpose cluster computing system System Tools
sparsehash extremely memory-efficient hash_map implementation Programming Tools
sphinx tool that makes it easy to create intelligent and beautiful documentation Libraries
splicegrapher prediction of alternative splicing patterns Bioinformatics
sqlcipher database encryption for SQLite Data Analysis
sqlite SQL database engine Data Analysis
sqliteman sqlite3 admin tool Data Analysis
sqliteodbc odbc wrapper for sqlite Data Analysis
sratoolkit access data from sequence read archive Bioinformatics
stack Haskell tool stack Programming Tools
stampy mapping of short reads onto a reference genome Bioinformatics
stata data analysis and statistics Data Analysis
stride integrates string and de Bruijn graph by decomposing reads within error-prone regions Bioinformatics
stringtie transcript assembly and quantification for RNA-seq Bioinformatics
subversion open source version control system Programming Tools
suitesparse suite of sparse matrix algorithms Libraries
sundials suite of nonlinear and differential/algebraic equation solvers Mathematics
swig interface compiler Programming Tools
tabix utilities for SAMtools Bioinformatics
taco multi-sample transcriptome assembly from RNA-seq Bioinformatics
tandem X! Tandem spectrum modeler Chemistry
tar create archives System Tools
tcl Tcl (Tool Command Language) is a very powerful but easy to learn dynamic programming language Programming Tools
tclap templatized C++ command line parser Programming Tools
tcllib The Tcl Library is a kitchen sink of packages across a broad spectrum of things Libraries
temp detecting transposable elements, insertions and absences from pooled high-throughput sequencing data Bioinformatics
texinfo official documentation format of the GNU project System Tools
texlive TeX document production system Accessories
tiff TIFF Library and Utilities Libraries
tinker molecular mechanics and dynamics with special features for biopolymers Molecular Biology
tk Tk is a graphical user interface toolkit that takes developing desktop applications to a higher level than conventional approaches Programming Tools
tmux terminal multiplexer System Tools
tophat fast splice junction mapper for RNA-Seq reads Bioinformatics
torch scientific computing framework for luajit Programming Tools
toyz Toyz for Data Analysis and Reduction Data Analysis
transdecoder find coding regions within transcripts Bioinformatics
tree list contents of directories in a tree-like format System Tools
trf Tandem Repeats Finder Bioinformatics
trimgalore quality and adaptor trimming for RRBS or standard FastQ files Bioinformatics
trimmomatic flexible read trimming tool for Illumina NGS data Bioinformatics
trinityrnaseq RNA-seq de novo assembly Bioinformatics
turbovnc offshoot of TightVNC that accelerates the Tight and JPEG encoding paths of the latter, in part by taking advantage of libjpeg-turbo, a SIMD-accelerated version of libjpeg System Tools
ucsc genome browser command-line tools Bioinformatics
unicycler hybrid assembly pipeline for bacterial genomes Bioinformatics
unison file synchronization System Tools
unixodbc open specification for data sources Data Analysis
unrar archive manager System Tools
unzip ZIP extraction Accessories
valgrind debugging and profiling Programming Tools
vardict sensitive variant called for both single and paired sample variant calling from BAM files Bioinformatics
varianttools software tool for the manipulation, annotation, selection, simulation, and analysis of variants in the context of next-gen sequencing analysis Bioinformatics
varscan variant detection in next-generation sequencing data Bioinformatics
vcflib simple C++ library for parsing and manipulating VCF files Bioinformatics
vcftools package for working with VCF files Bioinformatics
vdjer B Cell Receptor Repertoire Reconstruction from short read mRNA-Seq data Bioinformatics
velvet sequence assembler for very short reads Bioinformatics
velvetoptimiser Perl script for automatically optimizing the three primary parameter optinos for the velvet de novo sequence assembler Bioinformatics
vicare implementation of Scheme language compliant with R6RS standard with several language extensions Programming Tools
vienna prediction and comparison of RNA secondary structures Bioinformatics
virtualgl OpenGL interposer that allows applications to use remote display hardware Libraries
virusseq detection of known viruses and integration sites Bioinformatics
visit Open Source, interactive, scalable, visualization, animation and analysis tool Graphics
visualsfm GUI application for 3D reconstruction using structure from motion Graphics
vmd visual molecular dynamics Graphics
volview open-source, intuitive, interactive system for volume visualization that allows researchers to quickly explore and analyze complex 3D medical or scientific data Graphics
voro Voronoi diagram Mathematics
votca VOTCA is a software package which focuses on the analysis of molecular dynamics data, the development of systematic coarse-graining techniques as well as methods used for simulating microscopic charge and exciton transport in disordered semiconductors. Its C++ core is interfaced to bash and perl flow-control scripts Molecular Biology
vpnc virtual private network consortium Internet
vtk visualization toolkit Graphics
vxl collection of C++ libraries designed for computer vision research and implementation Libraries
wannier90 maximally-localized Wannier functions Chemistry
waveplot visualization of results fom DFTB+ Chemistry
weblogo create sequence logos Bioinformatics
weka machine learning algorithms for data mining Data Analysis
westpa The Weighted Ensemble Simulation Toolkit with Parallelization and Analysis Molecular Biology
wgs whole-genome shotgun assembler Bioinformatics
wine compatibility layer for Windows apps - 32 bit System Tools
wx cross-platform GUI library Libraries
wxPython a blending of the wxWidgets C++ class library with the Python programming language Libraries
wxwidgets cross-platform GUI library Programming Tools
x-devel X windows devel pkgs Libraries
xblas eXtended precision Basic Linear Algebra Subroutines Libraries
xcb X protocol C-language Binding (XCB) Libraries
xcrysden X-window CRYstalline Structures and DENsities Chemistry
xdmf Extensible Data Module and Format, a data model, library and file format for storing and managing data Libraries
xerces-c XML parser Programming Tools
xls2csv converts xsl files to csv - perl version System Tools
xpdf PDF viewer Accessories
xterm Xwindow terminal System Tools
xz free general-purpose data compression software with high compression ratio Libraries
yaehmop Yet Another extended Huckel Molecular Orbital Package Chemistry
yasm Yasm assembler Programming Tools
zint barcode generator Libraries
zlib Compression Library Libraries
zmq ZeroMQ lightweight messaging kernel Libraries